Mass Effect: Return from the Darkness
by hughcri
Summary: -I have planned for this story to be restarted on a smaller scale as the invasion seems to hard to believe- It has been Three years since Shepard disappeared, Three years since the Reapers returned to Dark Space and Three years for the Leviathan's to plan their return. Beta-Read by Stealer-L1F3
1. Chapter 1: The Prolouge

2189 CE Alliance Storage Facility Alpha March 9th3 years after Reaper War

It had been three years since the war with the reapers, three years since the disappearance of Shepard and the galaxy was still cleaning up. Franklin Jones worked for the newly formed "Alliance recovery unit"

The word Alliance was once used as the name for the human military but now was used for every race in the galaxy. A united alliance, a brand new era and he was stuck transporting crates. They had been charged with the safe transportation of the "Leviathan Orbs" he had no idea what they were but they seemed to him like a load of rubbish.

He sighed "When will we do something interesting" he said as he loaded another crate onto the back of a truck.

His friend Lia T'Sari sighed "Our job is to help the galaxy recover, the first step is too clear up all this rubbish" said the Asari as she loaded another crate.

"I know but I thought we would help rebuild colonies, help victims cope with their loss, not moving a load of crystal balls" he lifted the next crate onto the truck "Okay that is it!" the truck drove into the tunnel system linking them to their ship.

An alarm rang throughout the complex "Lunch Break!" he sat down on a couple of crates and opened up his bag.

Lia sighed, it had been a long three years, it seemed like it was just yesterday she had seen the reapers return to dark space. "Hey Frank?" she looked over at him. No reply "Frank?" the man just sat there, his face emotionless "Haha Frank, not funny"

Frank looked up at her and smiled, the crates behind him shon a brilliant blue. Then Frank spoke with a voice that was not his own "We will return from the Darkness"

…

Earth, March 12thT'soni apartment

The Shadow Broker sat at her desk as she searched her data-network. She scrolled through the information concerning the storage facility incident "The transportation of a classified cargo? Glyph!"

A small info drone hovered into the room "Yes Dr. T'Soni?"

"Find all information you can on this Cargo"

"Yes Dr. T'Soni"

The Asari sighed taking a sip of her coffee "Yuck!" she spat it out, she forgot it had been sitting there for over twelve hours. She wiped her mouth and walking into her living room. She looked up at the clock "By the goddess, was I really up all night?"

She groaned , Feron had offered to take some of her workload but she had refused "Glyph call Feron" a hologram of the Drell appeared before her.

"Oh hey Liar…I mean Shadow Broker, how may I help you"

"Feron, this workload is driving me insane, can I take you up on your offer"

"Sure, hold on" he tapped a few keys "Done"

Liara had become a very reclusive person since Shepard died. She spent most of her days cataloguing data and drinking cold coffee. Her friends had expressed concern but she convinced them she was fine. It had been ages since she last talked to Garrus, Joker, Tali. She sighed before walking to her bed.

…

Earth Outer Atmosphere, Destiny Ascension March 12th

Admiral Hackett's checked the reports, a scouting party had gone missing in the Psi Tophet system an hour ago and their last transmission was too static filled to hear anything. "Admiral Hackett sir" said a young woman knocking on the door.

"Yes?"

"You will want to see this"

….

In the Holo-Room a cluster of people watched a transmission from the lost ship. A deep voice filled the room "The sea is our home but the land is yours. We will help you recover from our creations destruction. You will serve us or perish" the video then showed a countdown timer "3 days, 7 Hours, 4 Minutes"

"What does this mean?" said one of the fellow admiral's

Hackett sighed "Another War"


	2. Chapter 2: Preparation

Despoina, Alliance ship March 12th

"Wha?" John Jones had been member of the ship's scouting party. Ever since the Reaper war the Alliance was on high alert and thus they had been en route to investigate a disturbance in Sigurd's cradle. It seems now they will never reach their objective. He groaned he rose off the floor, the ship was a wreck, water flooding in from all directions.

He clutched his side as he started to make his way through the wreckage. What could have caused all this damage? He thought. It looked like they had been used by a savage animal as its chew toy. He grabbed hold of a ladder before him and climbed it to the upper level. A loud quaking shot through the ship causing him to nearly loose his grip. He sighed as he climbed up into the hallway at the top, shaking and coughing. He looked up ahead and saw a familiar body on the floor "Cal?" Jonathan jumped up and sprinted to his friend "Cal, wha…" Cal's face was covered in what looked like coral and other underwater growth. Cal coughed weezily, his face spewing out nauseas white goo.

Jonathan nearly looked away "Oh my God, what happened?!"

Cal slowly turned his neck to Jonathan, his eyes blank and dead "Help….me" he rasped "Kill…me!"

"What? No!" he noticed the growth un his face seemed to go underneath the skin. A series of dark veiny markings spread down his neck disappearing beneath his collar. John searched around and grabbed a piece of glass "Cal, just stay still and this shouldn't hurt" he took a deep breath before dragging the glass across the man's uniform. What he saw underneath was rather unpleasant; his body was bony and glowing. His skin was bumpy and ragged. It reminded him of a reaper husk. Jonathan inspected the markings when…

"What the hell!" shouted John as Cal reached around the man's neck " It is me John! Your best…" Cal threw him across the hall like a ragdoll "Friend!" he fell through a glass window falling into a hangar type room. He groaned from the long fall, feeling like his back had shattered into a million pieces.

John slowly attempted to open his eyes. Grunts and snorts could be heard all around "Huh?" he looked up and saw a large creature. Its spine was partially exposed and his jaw was bearly holding on. It reminded him of a Reaper brute except with some major differences. It's claw arm reminded him of a shark, it had razor sharp teeth and a stretched out eye.

It's head had gills and its torso structure looked like a whale skeleton. Almost as if something had merged all these creatures together in a sick experiment. "Who…or what are you?"

The room was full of the things, accompanied by husks similar to Cal. The creature spoke it's voice had a demanding presence "Our name is beyond your understanding" It made John's ears ring almost like it was reaching into his brain "The nearest translation you humans have is Leviathan, a word originating from the so called human bible. A sea monster, except unlike monsters" it reached out and clamped its hand John's neck lifting him till they were face to face "We are very real" It slowly raised its claw arm…

Earth Outer Atmosphere, Destiny Ascension March 12th

All the Admirals just stared blankly at the display before them that had seconds ago played the message.

"It has to be a trick! Te…terrorists maybe. Batarians! They have grough voices!" stuttered one of the Admirals

"No!" shouted Hackett "We can't go about blaming random people." He took in a long sigh "Back when Shepard was alive…"

"Shepard, Shepard, Shepard! All you took about is John fucking Shepard! If you haven't realised Shepard is dead! KIA!" replied another one of the Admirals. He had aged greying hair, less extensive than Hackett's own.

"He is reported! As M.I.A! Missing in Action! And this isn't about him" replied Hackett "When Shepard was alive told us about Leviathan. The creator of the Reapers…" The crowd went silent"

The silver haired stuttered "The…the creators? Of the Reapers?"

Noise filled the crowd, "They live underwater as he said" _The sea is our home _"They controlled the other surface race's" _Land is yours_... "You will serve us_"_

One of the others sighed and finished "Or Perish"

"We have to prepare, now!"

Hackett sighed as he was passed a Data-pad "This is all the information we have on the Leviathan's"

…

Thessia Nyx Labs

Dr. Ann Bryson sat quietly on at her desk. After the end of the war she had nothing more to do with the Reapers or their creators. With the destruction of Task Force Aurora she created Nyx labs. They did all manner of research, but no matte how many things she did. She was still the galaxy's leading expert on one subject….

"The Leviathans"

Ann froze as Hackett spoke the words over her phone "Why are you calling me?"  
"You know why" Bryson stood up and walked into her hallway as she continued the conversation"

In the lab's main lobby was an almost exact replica of the marking's found by Aurora at Namakli. She examined the image of the beast and sighed "How long do we have?" Hackett was silent before finally saying.

"Three days" Ann froze and felt faint "I'll come in straight away"

Ann knew how little was known about the Leviathan, only one person ever met them and he was dead. To understand their power they would need to look back at their creation. The destroyer on Rannoch was in the best shape given it hadn't been destroyed by the Crucible. She would start there.

…

The Alliance had a series of ships at each Mass Relay and were tightening their defences. The relays were the most likely form of transportation the Leviathan's would use. Hackett checked the countdown, Only two days left, to bad for him they would be the quickest two days in his life.


	3. Chapter 3: Arrival

2189-CE 

Mass Relay 

March 14th

Day of Invasion

Admiral Hackett looked out of the main viewing port as he stood on the bridge of the Alliance Winged Ascent. Hundreds of Frigates surrounded the Sol relay. "Sir! Count down timer ending in three minutes!"

"Can you get through to Ann?"

"Sorry sir, the net is filled with traffic, when we can get through I will let you know"

"Are you telling me the Leviathans will arrive in less than three minutes and we have no communication with anyone?"

"There is the rest of the battle fleet sir"

Hackett growled and pinched the brim of his nose. How long?"

"Two minutes thirty eight"

"Patch me with the rest fleet" the lieutenant did as asked and the admirals voice boomed through every ship in miles "This is Admiral Hackett" In…he checked the timer the lieutenant had brought up "Two minutes, they will be upon us"

"Do not falter, do not be afraid! This is the moment of truth! These are the same beings that created the Reapers! BUT! They are the same beings that hid in the shadows will countless races were destroyed!"

"We shall be victorious!" Hackett sighed, wondering whether he believed his own speech or not. "Thirty seconds!" he looked ahead at the Sol relay, it felt like just yesterday they had broke it free of its icy prison. "Ten seconds!"

The crew hoped for the best"

"Nine!"  
"Eight!"

"Seven!"  
"Six!"  
"Five!"

"Four!"

"Three!"

"Two!"

"One!"

Now with no connection with the rest of the galaxy, it was a waiting game. Minutes passed in what felt like hours. Then it started, the concentric rings of the relay began to spin one by one. "This is it people!"

"Main cannons online!" A surge of energy spread out through the relay and straight at the fleet. "It is heading towards Contact One!" The pulse of energy hit the ship sending it into a slow drift.  
"Admiral Hackett! C1's systems offline!" The crewman was right, the entire ship had shut down, the crew had an hour of Oxygen left at most.

The relay surged up again and a grey metallic hulk emerged, it was the missing scout ship. "What is this?!" The ship was scared and broken, sea growth spread over its hull. Huge gaping holes ripped through it's outer shell.

"Unknown alliance asset! Respond!"

A deep distorted message filled the speakers "Lieutenant! Can you clean that up?"

"Yes, Hold on, there!"

A message played on loop "The sea is our home but the land is yours. We will help you recover from our creations destruction. You will serve us or perish. The sea is our home but the land is yours…."

"Oh no…."

Hundreds of the Leviathan brutes climbed out of the ghost ship. "Contacts! Lots of Contacts!" The creatures moved through the Vacuum like it was nothing. The creatures climbed up over the hull to the front. Hackett watched as they split into groups and jumped to the other cruisers "They are heading for C-1!"

"One rupture and the entire ship is dead! Fire!" the beasts glided through space. Shooting gases and other mixtures to propel themselves. The fleet destroyed as many as they could but not before one impacted the Contact's windows"

"Contact One is down! Contact one is down!" Hackett's eyes grew to the size of saucers when he saw large organic arms climb through the relay.

…

Evacuation of the civilian population had begun day two of the three. There was still huge chunks of the populous were still unaware of recent events. Liara T'Soni sat in her favourite chair. Sleeping as her computer complied all the information she had brokered. She didn't sleep often and when she did she was often plagued by nightmares.

_Hammer made one final sprint to the beam, surrounded by Mako's and sheer unrestrained force. Shepard lead the charge, a Mako flew through the air with a mighty roar. She froze as it roared overhead, Javik stood beside her, they jumped out of the way just in time. She sat there, as realisation hit her, she looked down to see a gaping hole in her stomach._

_The world around her was comprised by shadows. A oily shape of the Normandy flew in and around the battlefield. Harbinger just stood there, paying no attention to the Normandy, letting it fly in. She was tugged away towards the Normandy "Shepard…"_

_Harbinger still ignored the Normandy, he must have been keeping attention on the rest of Hammer, no it seemed like something more was at work. "You got to get out of here" Shepard's voice stood out from the ringing noise._

"_I'm alright, Shepard" she argued_

"_Don't argue with me Liara!" _

"_You're not leaving me behind"_

"_No matter what happens"_

"_You mean everything to me Liara. You always will"_

"_Shepard, I…I am yours"_

_Shepard looked to Harbinger as the Reaper stood there. "Go!" the Hanger bay door closed. But Liara's vision stayed with Shepard. What? She began to realise she was dreaming. Shepard ran to the beam, lasers and beams flew passed him. He leaped into the blinding light as the beam crumbled._

_Explosions resonated across the citadel and a great beam of blue energy extended from the star shaped installation. In the centre of the light emerged a crumpled body, his armour burnt and skin blistered. A N7 Logo embossed on his chest "Liara…"_

Liara's head flew up "By the Goddess" Her computer beeped at her, she pressed a key silencing it. She bought up a new tab "Feron…my evac shuttle still has not arrived, alert me as soon as you get this message" As the Shadow Broker it was her job to know everything, including a certain impending war.

She slid out of her chair and stretched, shed pinched her nose when it hit her. "What is that commotion" she strode over to the window and ripped the curtains open. People were running but running from what? "Aaaa!" a woman jumped onto her window scratching for entrance. Liara was about to let her in when her skin melted off of her face and her flesh burnt away leaving only a charred skeleton.

Liara stifled a gasp with her hands. She lowered her hands and lowered her eyebrows in determination. She ripped open the door and ran into the street, a giant figure descended from the sky. She stepped back and ran in the opposite direction. Beams of green and blue light ripped through the street tearing people apart.

Great fires spread and "Aaa!" she got distracted for too long and something tackled her to the ground. Her eyes filled with dread as a husk loomed over her. It was a olive drab colour and illuminated a florescent green light. A bright blue rose from her skull and travelled along her skin into the husk. The husk screeched in pain as it ascended through the sky.

She stared into the bright green sky. The Cuttlefish shaped being was getting closer. She rose her knees and crawled into a jog. A large crater came into sight. She lowered to her knees and peaked over the edge. A bunch of human Alliance soldiers had set up a base of sorts. She slid over the edge and into the pit.

"Miss! Stay close to us" Liara nodded.

"Why wasn't the city evacuated?!...Er…Mister?" The solider looked into the sky, wide eyed. Liara followed his line of vision, the Leviathan was coming closer, its feet to the city. It's trajectory had changed, it was heading straight for them. Its bony shelled feet impacted the city street.

The creatures eyes glowed a magnificent blue. Liara felt her head spin _Serve us… _Her trance came to an abrupt stop as the Leviathan fell back into the ocean. Liara's breath caught as she heard the familiar mechanic groan, behind her stood a Reaper, about the same size as the Leviathan. A hatch on its surface opened and out slid a bright red eye. The Solider stared at Liara.  
"What are you?" The Reapers eye was focused on her.

The reaper slumped down as if defeated and a loud hiss filled the air. A blinding light shone through the steam. The light shrunk into a scatter of blue lights, the lights were shaped as a humanoid, a humanoid that stepped into the open. "She…Shepard?!"

The man stood there like a god, Liara felt tears form in her eyes. The man slowly walked down to the blue Asari. "Liara" he awkwardly put his hand to her blue cheek. Liara closed her eyes at the contact. It was over before it began and Shepard was behind her with his sniper levelled at a Husk's head. Panels on the Reaper slid open revealing a shining red eye that decimated the Leviathans toys.

Shepard stepped down "We have to go!"  
One of the soldiers walked up to Shepard "Who the hell do you think you are and why are you with a Reaper?!"

One of the others grabbed the Marine by the shoulder "Dude! That is Commander Shepard"

"No way…"

Shepard noticed the vehicle to the left "Does that Mako work?"

"Er…yeah"

"Good and given the fact I don't feel you will be combatable riding inside a Reaper" he looked around the crater. "Well…Let's get moving"


End file.
